Regardless of whether an app purchased outside the MAS shows as installed, or does not show as installed in the MAS, they will not be available for
update through the MAS. That is the way the MAS program works. And I am sure that this was thought through on the part of Apple, knowing they would make some folks upset with the policy.
If an app developer has made previous commitments to its customers is not an Apple issue if the developer now chooses to not honor those commitments and deal exclusively with distributing their apps through the MAS. Reputable developers are continuing to provide
updates to their customers in their usual product streams.
There is a difference in an
update (v1.5 to v1.6) and an
upgrade (v5 to v6). Some developers may choose to continue to support minor updates to their current products through their normal streams and now the MAS, but may elect to offer all future new products and all major upgrades to an existing product exclusively through the MAS. One example of this is the developer of Pixelmator. They are continuing to offer free updates to the current app through their normal product distribution streams. However, they intend to only offer the next major upgrade to their product through the MAS. If customers elect to opt into the MAS they will have to purchase the product again, but it is being offered at a discount to the current retail price and as a further incentive to opt into the MAS, the next major upgrade will be available to MAS customers as if it were a free update.
Dah•veed